Pfam(http://pfam.sanger.ac.uk/)是一个被广泛使用的蛋白家族数据库，在最新的版本26.0中包含超过13000个手工确定的蛋白家族，Pfam可以通过http://pfam.sanger.ac.uk/使用，他有两个数据库，高质量，手工确定的Pfam-A，自动注释的Pfam-B数据库。后面的数据产生是根据ADDA算法。是对A的补充。

下载：

应的数据库(ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/)，按照说明说我下载的是

Pfam-A.hmm

Pfam-A.hmm.dat

Pfam-B.hmm

Pfam-B.hmm.dat

active_site.dat

HMMER3 (http://hmmer.janelia.org/software)

前准备工作：

Perl 和bioperl的安装 我的已经安装过了，据说可以通过一下方法安装

sudo

apt-get install perl ( replace perl with bioperl for installation

of bioperl)

Moose的安装

sudo -i ( the system will ask for

password type it in and youll find the user name change to root

marked in red. its ready to go now)

(因为之前没有权限，没用这一步，所以安装不来，导致后面的报错)

then use CPAN to install Moose use this:

CPAN Moose ( this will take a while)

HMMER3的安装

HMMER用来寻找同源序列数据库，做序列比对，它可用一条序列来寻找数据库，功能非常强大。

tar zxf hmmer-3.1b1.tar.gz

cd hmmer-3.1b1

./configure

make

make check

make install

cd easel;make install

修改环境变量：export

PATH=/sam/hmmer/binaries:$PATH(这个是针对bash而言的)

这个时候可以通过在终端输入：hmmscan -h 来检验是否安装成功

这就可以了嘛，不用怎么安装，修改环境变量即可。

export PERL5LIB=/sam/hmmmer/pfamscan:$PATH

(含有pfam_scan.pl)

(the path to your pfam_scan.pl should be listed if it is

successfully added)可以通过如下命令来查看环境变量是否修改成功

perl -V

为什么用的是PERL5LIB而不是PATH呢

What we’re doing in a nutshell is telling PERL to push values

on to the @INC array before loading any modules. You can do this on

the command line, in your PERL code or with the environment

variable PERL5LIB.

PERL5LIB can contain more than one value. Just set it in you

.bashrc file or wherever you see fit. This method works in

bash:

export

PERL5LIB=/first/path/to/libs"${PERL5LIB:+:$PERL5LIB}"

通过hmmerspress来把下载的数据建库:

hmmpress Pfam-A.hmm

hmmpress Pfam-B.hmm

使用说明：

pfam_scan.pl -fasta -dir

Additonal options:

-h  : show this help

-o  : output file, otherwise send to STDOUT

-clan_overlap  : show

overlapping hits within clan member families (applies to Pfam-A

families only)

-align  : show the HMM-sequence alignment for each

match

-e_seq  : specify hmmscan evalue

sequence cutoff for Pfam-A searches (default Pfam defined)

-e_dom  : specify hmmscan evalue

domain cutoff for Pfam-A searches (default Pfam defined)

-b_seq  : specify hmmscan bit score

sequence cutoff for Pfam-A searches (default Pfam defined)

-b_dom  : specify hmmscan bit score

domain cutoff for Pfam-A searches (default Pfam defined)

-pfamB  : search against Pfam-B HMMs (uses E-value

sequence and domain cutoff 0.001),

in addition to searching Pfam-A HMMs

-only_pfamB  : search against Pfam-B HMMs only (uses E-value

sequence and domain cutoff 0.001)

-as  : predict active site residues for Pfam-A

matches

-json [pretty]  : write

results in JSON format. If the optional value "pretty" is

given,

the JSON output will be formatted using the

"pretty" option in the JSON

module

For more help, check the perldoc:

shell% perldoc pfam_scan.pl

例如：

/sam/hmmer/PfamScan/pfam_scan.pl -fasta contig_proteins.fasta

-dir /sam/hmmer/PfamScan/lib -pfamB -out contig_pfam.fasta

注释出来的结果中含有.后面跟的数字与不跟数字有什么区别？？

pfam-help@ebi.ac.uk

There is no difference for the user.

The extra numerals after the . are for internal auditing and

have no meaning

for the results. In effect both are PF00013.24 - that is:

version 24 since

first creation of family.

结果的初步解读：

# < seq id> < alignment start> < alignment

end> < envelope start> < envelope end> < hmm

acc>

< hmm name> < type> < hmm

start> < hmm end> < hmm length> < bit score>

< E-value> < significance>

< clan>

1_1  111  424

110  425 PF01979.15  Amidohydro_1

Domain

2  332

333  185.8  1.5e-54

1 CL0034

1_2  30  130

30  130 PF13600.1  DUF4140

Family  1  104

104  52.1  6.7e-14  1 No_clan

这里的PF代表的是pfam-A,PB代表的是pfam-B数据库。

clan表示上一级的分类

利用官网首页"Jump to”功能，检索注释出来的详细的信息：

Pfam A accession, e.g. PF02171

Pfam A identifier, e.g. piwi

Pfam B accession, e.g. PB000001

Pfam B identifier, e.g. Pfam-B_1

UniProt sequence accession, e.g. P00789

UniProt sequence ID, e.g. CANX_CHICK

NCBI "GI" number, e.g. 113594566

NCBI secondary accession, e.g. BAF18440.1

Pfam clan accession, e.g. CL0005

metaseq ID, e.g. JCVI_ORF_1096665732460

metaseq accession, e.g. JCVI_PEP_1096665732461

Pfam clan accession, e.g. CL0005

Pfam clan ID, e.g. Kazal

PDB entry, e.g. 2abl

Proteome species name, e.g. Homo sapiens

之前的邮箱不好使了。

pfamlist-subscribe@sanger.ac.uk

参考资料：文献:The Pfam protein families database

官网说明说 readme

ps:  1,pfam团队的邮箱：pfam-help@sanger.ac.uk。有问题就可以问他们

2，Can't locate Bio/Pfam/Scan/PfamScan.pm in @INC

(@INC contains: /etc/perl /usr/local/lib/perl/5.14.2

/usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5

/usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .)

at /sam/hmmer/PfamScan/pfam_scan.pl line 8.

BEGIN failed--compilation aborted at

/sam/hmmer/PfamScan/pfam_scan.pl line

8.这个问题折腾了我很久，最后我改了两点，一个就是通过cpan下载Moose,另一个就是修改了pfam_scan.pl的环境变量，就OK了。那就根据我博文中提到的PERL5LIB，我觉得应该是第二个原因。反正问题解决了，who

care 呢？